This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. Abstract: We propose to continue to develop and enhance our AMBER software for parallel computers and to use this and other software to understand molecular recognition and enzyme catalysis in complex molecular systems involving proteins, nucleic acids and other molecules of biological interest.